Imaging active site chemistry and protonation states: NMR crystallography of the tryptophan synthase α-aminoacrylate intermediate

Author:

Holmes Jacob B.1,Liu Viktoriia1,Caulkins Bethany G.12,Hilario Eduardo1,Ghosh Rittik K.3,Drago Victoria N.4ORCID,Young Robert P.5ORCID,Romero Jennifer A.1ORCID,Gill Adam D.3,Bogie Paul M.1,Paulino Joana6,Wang Xiaoling6ORCID,Riviere Gwladys7ORCID,Bosken Yuliana K.3ORCID,Struppe Jochem8ORCID,Hassan Alia9,Guidoulianov Jevgeni9,Perrone Barbara9,Mentink-Vigier Frederic6ORCID,Chang Chia-en A.1ORCID,Long Joanna R.7,Hooley Richard J.13,Mueser Timothy C.4ORCID,Dunn Michael F.3,Mueller Leonard J.1ORCID

Affiliation:

1. Department of Chemistry, University of California, Riverside, CA 92521;

2. W.M. Keck Science Department, Claremont McKenna, Pitzer, and Scripps Colleges, Claremont, CA 91711;

3. Department of Biochemistry, University of California, Riverside, CA 92521;

4. Department of Chemistry and Biochemistry, University of Toledo, Toledo, OH 43606;

5. Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA 99354;

6. National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL 32310;

7. Department of Biochemistry and Molecular Biology, McKnight Brain Institute, National High Magnetic Field Laboratory, University of Florida, Gainesville, FL 32610;

8. Bruker Biospin Corporation, Billerica, MA 01821;

9. Bruker Switzerland AG 8117 Fällanden, Switzerland

Abstract

Significance The determination of active site protonation states is critical for a full mechanistic understanding of enzymatic transformations. However, hydrogen atom positions are challenging to extract using the standard tools of structural biology. Here, we make use of a joint solid-state NMR, X-ray crystallography, and first-principles computational approach that enables the investigation of enzyme catalysis at this fine level of chemical detail. For tryptophan synthase, this allows us to peer along the reaction coordinates into and out of the α-aminoacrylate intermediate. Through this process, we are developing a high-resolution probe for structural biology that is keenly sensitive to hydrogen atom positions—complementing diffraction methods yet able to be applied under conditions of active catalysis in microcrystalline and non-crystalline materials.

Funder

National Science Foundation

HHS | National Institutes of Health

Publisher

Proceedings of the National Academy of Sciences

Subject

Multidisciplinary

Reference84 articles.

1. C. Walsh, Enzymatic Reaction Mechanisms (W. H. Freeman and Company, San Francisco, 1979), pp. 978.

2. Pyridoxal Enzymes: Mechanistic Diversity and Uniformity

3. A genomic overview of pyridoxal‐phosphate‐dependent enzymes

4. Controlling reaction specificity in pyridoxal phosphate enzymes

5. Tryptophan synthase: Structure, function, and subunit interaction;Miles E. W.;Adv. Enzymol. Relat. Areas Mol. Biol.,1979

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